Sodium in PDB 6ubh: Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide

The structure of Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide, PDB code: 6ubh was solved by A.U.Singer, J.Teyra, M.Mclaughlin, A.Ernst, F.Sicheri, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.77 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.000, 39.010, 58.380, 72.55, 72.61, 96.06
R / Rfree (%)	19.7 / 22.5

The binding sites of Sodium atom in the Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide (pdb code 6ubh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide, PDB code: 6ubh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:28.9 occ:1.00 O A:ASP51 2.4 21.8 1.0 O C:SER20 2.9 15.8 1.0 O A:HOH382 3.0 21.8 1.0 C A:ASP51 3.5 20.6 1.0 CB A:ASP51 3.9 23.1 1.0 CB C:SER19 3.9 22.4 1.0 N C:SER20 4.0 20.9 1.0 C C:SER20 4.0 17.2 1.0 O C:HOH360 4.2 20.0 1.0 CA A:ASP51 4.3 21.3 1.0 N A:ASP52 4.4 19.6 1.0 OG C:SER19 4.5 21.8 1.0 CA A:ASP52 4.5 17.7 1.0 CA C:SER19 4.5 21.1 1.0 C C:SER19 4.6 21.6 1.0 CA C:SER20 4.7 15.9 1.0

Sodium binding site 2 out of 3 in the Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:21.1 occ:1.00 OE1 C:GLU104 2.5 19.1 1.0 NH2 C:ARG26 2.8 17.7 1.0 OE2 C:GLU104 3.0 28.4 1.0 NH1 C:ARG24 3.1 17.2 1.0 CD C:GLU104 3.1 17.9 1.0 O C:HOH310 3.6 15.4 1.0 NE2 D:GLN78 3.7 15.6 1.0 CZ C:ARG24 4.0 18.7 1.0 CZ C:ARG26 4.1 18.4 1.0 NH2 C:ARG24 4.5 16.0 1.0 O C:HOH316 4.5 18.0 1.0 OE1 D:GLN78 4.6 13.7 1.0 O D:HOH312 4.6 15.8 1.0 CD D:GLN78 4.6 15.0 1.0 CG C:GLU104 4.6 17.6 1.0 NH1 C:ARG26 4.7 15.8 1.0 NE C:ARG24 4.8 17.9 1.0 NE C:ARG26 4.9 17.3 1.0 O D:HOH338 5.0 16.7 1.0

Sodium binding site 3 out of 3 in the Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the MM7 Erbin Pdz Variant in Complex with A High-Affinity Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:15.6 occ:1.00 OE1 D:GLN71 2.3 18.7 1.0 O D:HOH333 2.3 14.4 1.0 O D:HOH313 2.8 23.4 1.0 CD D:GLN71 3.4 16.7 1.0 CB D:GLN71 3.6 15.2 1.0 O D:PRO72 3.9 13.0 1.0 O D:HOH325 3.9 13.7 1.0 CG D:GLN71 4.0 12.7 1.0 CG D:ARG109 4.1 14.3 1.0 O D:HOH344 4.2 15.4 1.0 CD D:ARG109 4.2 13.8 1.0 NE D:ARG109 4.4 13.7 1.0 OD1 D:ASP74 4.4 13.7 1.0 NE2 D:GLN71 4.4 21.0 1.0 CA D:GLN71 4.9 14.4 1.0 C D:GLN71 4.9 13.9 1.0 C D:PRO72 5.0 14.7 1.0

J.Teyra, M.Mclaughlin, A.Singer, A.Kelil, T.-H.Kim, A.Ernst, F.Sicheri, S.S.Sidhu. Directed Evolution of Pdz Fold Specificity For A Single Peptide Position To Be Published.